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__init__(self,
basename=None,
cms_fn=None,
tmp_dir=None)
x.__init__(...) initializes x; see help(type(x)) for signature |
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get_cms(self,
cms_fn)
try to find cms file |
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parse_fep_data(self)
Given an ark object, parse the data |
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| read_FEPSimulation(self,
ark_obj) |
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| read_ProteinInfo(self,
ark_obj) |
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| read_LigandInfo(self,
ark_obj) |
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| read_FEP_REST_energetics(self,
ark_obj) |
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| read_REST_exchanges(self,
ark_obj) |
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| reportReplicaExchanges(self) |
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| reportReplicaPairEnergies(self) |
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| add_replicas_dF_table(self,
ark_obj) |
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| add_overlapEnergyTable(self,
data) |
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| getOverlapEnergyPlot(self) |
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| getEnergyConvergencePlot(self) |
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| reportLigandsDetails(self) |
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| reportProteinDetails(self) |
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getSequenceViewerImage(self,
prot_str)
Generate protein sequence image, given a protein structure Returns a
platipus image |
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| getTempImageFilename(self) |
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| getLigandImage(self,
asl_str,
lig_num) |
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| reportSimulationDetails(self) |
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str(self,
str_in)
This is to remove the "'s in ARK returned strings enclosed in
double quotes |
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Inherited from object:
__delattr__,
__format__,
__getattribute__,
__hash__,
__new__,
__reduce__,
__reduce_ex__,
__repr__,
__setattr__,
__sizeof__,
__str__,
__subclasshook__
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